SLC39A6

protein-coding

solute carrier family 39 member 6, the group of Solute carrier family 39

Gene summary

Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A6 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_012319.4

Inheritance

—

ClinVar variants

U:93B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr18:36,108,531-36,129,385

External References & Databases

Ensembl (ENSG00000141424)

Transcript & Mutation Effects

hg38 • Region Span ~20.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC39A6 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 90

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012319.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			88 clinvar	4 clinvar		92
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	93	4	0	97

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012319.4	RefSeq	NP_036451.4	9	MANE Select
ENST00000269187.10	Ensembl	ENSP00000269187.4	9	MANE Select
NM_001099406.2	RefSeq	NP_001092876.1	7	Standard
ENST00000440549.6	Ensembl	ENSP00000401139.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Nuclear Receptors Meta-Pathway
NRF2 pathway
Zinc homeostasis
Zinc influx into cells by the SLC39 gene family
Transport of bile salts and organic acids, metal ions and amine compounds

Biological Process

cellular zinc ion homeostasis
zinc ion transmembrane transport
zinc ion import across plasma membrane

Molecular Function

zinc ion transmembrane transporter activity

Cellular Component

endoplasmic reticulum
plasma membrane
integral component of plasma membrane
cell surface
lamellipodium membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000269187
Coding exons: 9
Length: 20854
Individuals with no LoFs: 124796
Homozygous LoFs: 1
Heterozygous LoFs: 39
Defined: 124836
p: 0.000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.13	346	410	0.843	0.0000214	5048
Missense (PolyPhen)		94	178	0.5281		2151
Synonymous	0.161	147	150	0.983	0.00000815	1420
Loss of Function	2.39	15	28.9	0.519	0.00000167	360

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000064	rare
Latino/Admixed American	0.00026	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00018	0.00017	rare
South Asian	0.00043	0.00029	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a zinc-influx transporter. {ECO:0000269|PubMed:12839489}.;

Recessive Scores

pRec: 0.123

Intolerance Scores

LoFtool: 0.701
RVIS EVS: -0.8
RVIS percentile EVS: 12.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.667

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium